Synchrotron radiation-based tomography of an entire mouse brain with sub-micron voxels: augmenting interactive brain atlases with terabyte data (2405.13971v3)

Abstract: Synchrotron radiation-based X-ray microtomography is uniquely suited for post mortem three-dimensional visualization of organs such as the mouse brain. Tomographic imaging of the entire mouse brain with isotropic cellular resolution requires an extended field-of-view and produces datasets of multiple terabytes in size. These data must be processed and made accessible to domain experts who may have only limited image processing knowledge. We present extended-field X-ray microtomography with 0.65 $\mu$m voxel size covering an entire mouse brain. The 4,495 projections from 8 x 8 offset acquisitions were stitched to reconstruct a volume of 15,000$^3$ voxels. The microtomography volume was non-rigidly registered to the Allen Mouse Brain Common Coordinate Framework v3 based on a combination of image intensity and landmark pairs. The data were transformed block-wise and stored in a public repository with a hierarchical format for navigation and overlay with anatomical annotations in online viewers such as Neuroglancer or siibra-explorer. This study demonstrates X-ray imaging and data processing for a full mouse brain, augmenting current atlases by improving resolution in the third dimension by an order of magnitude. The 3.3-teravoxel dataset is publicly available and easily accessible for domain experts via browser-based viewers.